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Sample GSM11014 Query DataSets for GSM11014
Status Public on Nov 15, 2003
Title CA5_FE3_bot
Sample type RNA
 
Channel 1
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, Clofibric Acid (0.5% w/w) treatment for 1 week
Organism Sus scrofa
Extracted molecule total RNA
 
Channel 2
Source name Porcine liver, 5 weeks, male, Yorkshire x Landrace, fed
Organism Sus scrofa
Extracted molecule total RNA
 
 
Description CA5_FE3_bot
 
Submission date Oct 04, 2003
Last update date May 28, 2005
Contact name Yewon Cheon
E-mail(s) yecheon@uiuc.edu
Phone 217-333-7371
Organization name University of Illinois at Urbana Champaign
Street address
City Urbana
State/province IL
ZIP/Postal code 61801
Country USA
 
Platform ID GPL518
Series (1)
GSE714 Porcine liver

Data table header descriptions
ID_REF
Block
Column
Row
X X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Y Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image
Dia. diameter in µm of the feature-indicator
F635 Median median pixel intensity of feature for Cy5 channel
F635 Mean mean pixel intensity of feature for Cy5 channel
F635 SD Cy5 pixel intensity standard deviation
B635 Median median Cy5 feature background intensity
B635 Mean mean Cy5 feature background intensity
B635 SD Cy5 background pixel intensity standard deviation
% > B635+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
% > B635+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm, Cy5)
F635 % Sat. percentage of pixel saturation within feature
F532 Median median feature pixel intensity at wavelength #2 (532 nm, Cy3)
F532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
F532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Median median feature background intensity at wavelength #2 (532 nm, Cy3)
B532 Mean mean feature background intensity at wavelength #2 (532 nm, Cy3)
B532 SD standard deviation of the feature background intensity at wavelength #2 (532 nm, Cy3)
% > B532+1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
% > B532+2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm, Cy3)
F532 % Sat. percentage of feature pixels at wavelength #2 (Cy3) that are saturated
Ratio of Medians (635/532) ratio of the background subtracted median pixel intensity at the second wavelength (Cy3), to the background subtracted median pixel intensity at the first wavelength(Cy5)
Ratio of Means (635/532) ratio of the arithmetic mean of the background subtracted raw pixel intensities at the second wavelength (Cy3), to the arithmetic mean of the background subtracted raw pixel intensities at the first wavelength (Cy5)
Median of Ratios (635/532) median of the pixel-by-pixel ratios of pixel intensities that have had the median background intensity subtracted of wavelength 2 (Cy3) to wavelength one (Cy5)
Mean of Ratios (635/532) arithmetic mean of the pixel-by-pixel ratios of the raw pixel intensities of wavelength 2 (Cy3) to wavelength 1 (Cy5)
Ratios SD (635/532) standard deviation of the log of pixel intensity ratios
Rgn Ratio (635/532) regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn R² (635/532) coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels number of feature pixels
B Pixels number of background pixels
Sum of Medians sum of the median of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
Sum of Means sum of the arithmetic mean of the pixel intensities at each wavelength, with the median background pixel intensity at each wavelength subtracted
VALUE Log ratio (635/532) - base two logarithm of the ratio of medians
F635 Median - B635 Cy5 median feature intensity subtracted by Cy5 median background intensity
F532 Median - B532 Cy3 median feature intensity subtracted by Cy3 median background intensity
F635 Mean - B635 Cy5 mean feature intensity subtracted by Cy5 mean background intensity
F532 Mean - B532 Cy3 mean feature intensity subtracted by Cy3 mean background intensity
Flags A value of -100 means that this spot was bad. A value of -75 means that the ID for this spot is empty. A value of -50 means that this spot cannot be aligned during analysis. A value of 0 or larger than 0 means that this spot passed the flagging screen but may still fail other quality tests.
Normalize

Data table
ID_REF Block Column Row X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R² (635/532) F Pixels B Pixels Sum of Medians Sum of Means VALUE F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 Flags Normalize
1 1 1 1 2720 50260 80 883 904 231 603 634 203 63 28 0 1151 1148 119 893 900 111 86 71 0 1.085 1.18 1.182 1.264 2.594 2.638 0.125 52 321 538 556 0.118 280 258 301 255 0 0
2 1 2 1 2910 50260 120 947 1148 1060 635 667 385 41 8 0 1218 1540 3076 891 903 152 79 56 0 0.954 0.79 1.074 1.086 3.276 0.044 0.01 120 607 639 1162 -0.068 312 327 513 649 0 0
3 1 3 1 3100 50240 120 1229 1247 340 627 663 395 75 24 0 1382 1440 259 865 877 147 95 89 0 1.164 1.078 1.06 1.021 2.212 1.428 0.392 120 636 1119 1195 0.22 602 517 620 575 0 0
4 1 4 1 3300 50230 110 1072 1065 301 592 611 195 87 55 0 1287 1275 169 849 866 174 93 65 0 1.096 1.11 1.098 1.033 2.054 1.528 0.31 80 576 918 899 0.132 480 438 473 426 0 0
5 1 5 1 3520 50220 120 2004 2054 1556 593 609 198 95 91 0 2483 2472 521 864 881 156 99 98 0 0.872 0.909 0.788 0.79 1.813 1.662 0.349 120 701 3030 3069 -0.198 1411 1619 1461 1608 0 0
6 1 6 1 3710 50220 110 2245 2286 472 547 588 259 100 100 0 2741 2787 365 841 883 228 100 100 0 0.894 0.894 0.888 0.876 1.36 0.887 0.768 80 543 3598 3685 -0.162 1698 1900 1739 1946 0 0
7 1 7 1 3910 50230 120 3167 3135 1030 560 600 295 98 96 0 2710 2703 716 824 849 180 98 96 0 1.382 1.37 1.38 1.344 1.635 1.429 0.821 120 646 4493 4454 0.467 2607 1886 2575 1879 0 0
8 1 8 1 4110 50230 120 3330 3278 969 614 630 190 99 98 0 2919 2827 672 846 858 144 98 95 0 1.31 1.345 1.331 1.359 1.671 1.404 0.844 120 632 4789 4645 0.39 2716 2073 2664 1981 0 0
9 1 9 1 4300 50230 110 3343 3258 596 605 654 562 100 98 0 3545 3488 492 850 889 381 100 100 0 1.016 1.006 1.005 0.992 1.326 1.189 0.671 80 541 5433 5291 0.023 2738 2695 2653 2638 0 0
10 1 10 1 4500 50250 120 2989 2963 859 634 684 513 97 90 0 3196 3098 620 843 877 354 100 98 0 1.001 1.033 1.046 0.982 1.542 1.099 0.834 120 672 4708 4584 0.001 2355 2353 2329 2255 0 0
11 1 11 1 4720 50260 110 2727 2688 602 552 582 204 100 100 0 3296 3296 529 805 824 195 100 100 0 0.873 0.857 0.874 0.838 1.313 0.887 0.813 80 588 4666 4627 -0.196 2175 2491 2136 2491 0 0
12 1 12 1 4920 50260 110 2934 2963 660 545 603 678 100 97 0 3435 3370 519 792 821 322 100 100 0 0.904 0.938 0.91 0.923 1.287 1.237 0.511 80 598 5032 4996 -0.146 2389 2643 2418 2578 0 0
13 1 1 2 2710 50430 110 668 696 205 592 604 183 30 11 0 1006 1038 238 871 885 137 46 17 0 0.563 0.623 1.101 0.99 4.862 6.616 0.006 80 576 211 271 -0.829 76 135 104 167 -50 0
14 1 2 2 2910 50430 110 788 790 203 614 635 193 43 16 0 1044 1062 186 898 908 135 51 18 0 1.192 1.073 1.268 1.384 4.346 2.788 0.055 80 528 320 340 0.253 174 146 176 164 -50 0
15 1 3 2 3110 50430 110 585 603 153 622 647 212 7 1 0 891 926 212 877 895 157 16 6 0 -2.643 -0.388 1.129 1.208 4.018 16.922 0.001 80 539 -23 30 -37 14 -19 49 -50 0
16 1 4 2 3310 50430 110 602 613 187 583 613 235 12 2 0 895 931 293 846 862 185 16 2 0 0.388 0.353 1.525 1.596 3.366 33.211 0 80 588 68 115 -1.367 19 49 30 85 -50 0
17 1 5 2 3520 50430 70 802 805 168 614 641 197 43 15 0 1198 1183 153 869 885 137 84 65 0 0.571 0.608 0.685 0.73 2.139 1.504 0.072 32 236 517 505 -0.807 188 329 191 314 0 0
18 1 6 2 3730 50430 90 801 848 231 545 567 272 48 15 0 1200 1204 199 812 837 158 84 65 0 0.66 0.773 0.933 0.791 2.697 3.88 0.082 52 396 644 695 -0.6 256 388 303 392 0 0
19 1 7 2 3910 50440 120 6815 7040 1721 559 575 176 100 100 0 5800 6000 1524 836 843 119 100 100 0 1.26 1.255 1.266 1.299 1.548 1.28 0.875 120 579 11220 11645 0.334 6256 4964 6481 5164 0 0
20 1 8 2 4110 50440 130 7828 7833 1484 577 599 188 100 100 0 6720 6516 1392 847 865 214 99 99 0 1.235 1.28 1.26 1.354 1.644 1.285 0.885 120 637 13124 12925 0.304 7251 5873 7256 5669 0 0

Total number of rows: 2880

Table truncated, full table size 517 Kbytes.




Supplementary data files not provided
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